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  1. IGB
  2. IGBF-1421

Add potato genome to IGB Quickload

        Details

        • Story Points:
          0.25
        • Sprint:
          Fall 2018 Sprint 3

          Description

          Add latest potato genome to quickload.

          Add

          • sequence data
          • latest gene models (from MSU)

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-1423 Add potato genome assembly synonyms to IGB species.txt

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. HELP-276 Potato genome and transcriptome

              • To-Do

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1420 Add open access potato image to IGB start screen

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment - - edited

                Added sequence data (2bit file) for DM1-3 version 4.03 assembly as S_tuberosum_DM_Jul_2011 genome version to subversion repo at https://svn.bioviz.org/viewvc.
                Added gene model annotations.
                Updated production Quickload sites:

                Show
                ann.loraine Ann Loraine added a comment - - edited Added sequence data (2bit file) for DM1-3 version 4.03 assembly as S_tuberosum_DM_Jul_2011 genome version to subversion repo at https://svn.bioviz.org/viewvc . Added gene model annotations. Updated production Quickload sites: http://igbquickload.org/quickload (main) http://lorainelab-quickload.scidas.org/quickload/ (backup)
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                ann.loraine Ann Loraine added a comment -

                To test:

                • Select Current Genome
                • Select species "Solanum tuberosum Group Phureja clone DM1-3"
                • Select latest genome

                Observe gene models load automatically.

                Check data:

                • Check that plus strand CDSs (thick part) start with ATG. Check every chromosome. Make note of any errors.
                • Check that minus strand CDSs start with ATG reverse complement. Check every chromosome. Make note any errors.
                • Check that sequence can be loaded.
                • Check that gene models overlapping the same region have the same "title" (gene name)
                Show
                ann.loraine Ann Loraine added a comment - To test: Select Current Genome Select species "Solanum tuberosum Group Phureja clone DM1-3" Select latest genome Observe gene models load automatically. Check data: Check that plus strand CDSs (thick part) start with ATG. Check every chromosome. Make note of any errors. Check that minus strand CDSs start with ATG reverse complement. Check every chromosome. Make note any errors. Check that sequence can be loaded. Check that gene models overlapping the same region have the same "title" (gene name)
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                ptambvek Pranav Sanjay Tambvekar (Inactive) added a comment -

                Tested according to the guidelines mentioned above. No errors observed

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                ptambvek Pranav Sanjay Tambvekar (Inactive) added a comment - Tested according to the guidelines mentioned above. No errors observed
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                ann.loraine Ann Loraine added a comment -

                Thanks for the fast turn-around!
                Please move to Done lane.

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                ann.loraine Ann Loraine added a comment - Thanks for the fast turn-around! Please move to Done lane.

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: